Authors: Carter, Phil¹; Liu, Jinfeng²; Rost, Burkhard²

Source: Nucleic Acids Research, Volume 31, Number 1, 01 January 2003 , pp. 410-413(4)

Publisher: Oxford University Press

Abstract:

PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life: eukaryotes, prokaryotes and archaea. All proteins publicly available for organisms were aligned against SWISS-PROT, TrEMBL and PDB. Additionally, the following annotations are provided: secondary structure, transmembrane helices, coiled coils, regions of low complexity, signal peptides, PROSITE motifs, nuclear localization signals and classes of cellular function. Proteins that contain long regions without regular secondary structure are also identified. We have produced a related database of structural domain-like fragments derived from PEP and clusters based on homology between all fragments. The PEP database, fragments and clusters are distributed freely as a set of flat files and have been integrated into SRS. The PEP group of databases can be accessed from: http://cubic.bioc.columbia.edu/pep.

Document Type: Research article

DOI: http://dx.doi.org/10.1093/nar/gkg102

Affiliations: 1: *To whom correspondence should be addressed., Tel: +1 2123053773, Fax: +1 2123057932, Email: carter@cubic.bioc.columbia.edu 2: CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA

Publication date: 2003-01-01

More about this publication?

• Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
  in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.

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